Man pages for BIGDAWG
Case-Control Analysis of Multi-Allelic Loci
| A | Amino Acid Analysis Function |
| AA.df.check | Contingency Table Check |
| AA.df.cs | Contingency Table Amino Acid ChiSq Testing |
| AAtable.builder | Amino Acid Contingency Table Build |
| AlignmentFilter | Alignment Filter |
| AlignObj.Create | Alignment Object Creator |
| AlignObj.Update | Updated Alignment Object Creator |
| Append.System | Append Genetic System Locus Designation to Allele String |
| A.wrapper | Amino Acid Wrapper |
| BIGDAWG | BIGDAWG Main Wrapper Function |
| buildHAPnames | Haplotype Name Builder |
| buildHAPsets | Haplotype List Builder |
| Build.Matrix | Build Output Matrix for GL2Tab Conversion |
| cci | Case-Control Odds ratio calculation and graphing |
| cci.pval | Case Control Odds Ratio Calculation from Epicalc |
| cci.pval.list | Case Control Odds Ratio Calculation from Epicalc list... |
| CheckAlleles | HLA Allele Legitimacy Check for Amino Acid Analysis |
| Check.Cores | Check Cores Parameters |
| Check.Data | Check Data Structure |
| CheckHLA | HLA Formatting Check for Amino Acid Analysis |
| CheckLoci | HLA Loci Legitimacy Check for Amino Acid Analysis |
| Check.Params | Check Input Parameters |
| Check.Params.GLS | Check Input Parameters for GLS conversion |
| CheckRelease | Function to Check Release Versions |
| CheckString.Allele | GL String Allele Check |
| CheckString.Locus | GL String Locus Check |
| Condense.EPL | Condensing Exon Specific Alignments to Single Dataframe |
| Create.Null.Table | Create Empty Table |
| DRB345.Check.Wrapper | DRB345 haplotype zygosity wrapper |
| DRB345.Check.Zygosity | DRB345 haplotype zygosity checker single locus |
| DRB345.Exp | DRB345 Expected |
| DRB345.parser | DRB345 Column Processing |
| Err.Log | Error Code Display and Logging |
| EVSremoval | Expression Variant Suffix Removal |
| Exon.Filter | Filter Exon Specific Alignment Sections |
| ExonPtnAlign.Create | Protein Exon Alignment Formatter |
| ExonPtnList | Exon protein alignments. |
| Filler | Replace or Fill 00:00 allele strings |
| Format.Allele | Ambiguous Alleles Locus Name Formatting |
| Format.Tab | Tabular Data Locus Format Tool |
| getAllele.Count | Recompute number of alleles |
| getCS.Mat | Chi square matrices |
| getCS.stat | Chi square test statistic |
| GetField | HLA trimming function |
| getFileName | File Name Extraction |
| GetFiles | File Fetcher |
| getHap | Haplotype Table Maker |
| getObsFreq | Observed Frequency |
| GL2Tab.Loci | Locus Ordering for GL2Tab |
| GL2Tab.Sub | Genotype List String Expander |
| GL2Tab.wrapper | Genotype List String to Tabular Data Conversion |
| GLSconvert | Genotype List String Conversion |
| HLA_data | Example HLA Dataset |
| H.MC | Haplotype Analysis Function for Multicore |
| H.MC.wrapper | Haplotype Wrapper for Multicore |
| HWE | Hardy Weinbergy Equilibrium Function |
| HWE.ChiSq | Hardy Weinbergy Equilibrium Function |
| HWE.wrapper | Hardy-Weinbery Wrapper |
| L | Locus Analysis Function |
| L.wrapper | Locus Wrapper |
| make2x2 | Creation of a 2x2 table using the indicated orientation. |
| makeComb | Genotype Combination Maker |
| MergeData_Output | Data Object Merge and Output |
| PgrpExtract | HLA P group Finder |
| PgrpFormat | HLA P group File Formatter |
| PreCheck | Data Summary Function |
| prepData | Prepare imported data |
| rmABstrings | Replace absent allele strings |
| RunChiSq | Strict Chi-squared Contingency Table Test |
| RunChiSq_c | Contextual Binning Chi-squared Contingency Table Test |
| Stripper | Removes System and Locus from Alleles |
| summaryGeno.2 | Haplotype missing Allele summary function |
| Tab2GL.Loci | Locus Condenser for Tab2GL |
| Tab2GL.Sub | Genotype List String Condenser |
| Tab2GL.wrapper | Genotype List String to Tabular Data Conversion |
| TableMaker | Table Maker |
| UpdateRelease | Update function for protein aligment upon new IMGT HLA data... |
